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What I'm unsecure about is what you mean with "shared cache store instance".
shared is a configuration option for the CacheStores :
https://docs.jboss.org/author/display/ISPN/CacheLoaders#CacheLoaders-Configuration
Basically you have to tell Infinispan if each node is going to be connected to the same store or if they are going to have independent stores. When shared, only one node will apply updates; when it's not shared each node owning a copy of the entry you wrote will write it.
In short if you configure it as shared but they are not in practice, you might lose data.
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I am still wondering then where the sync problems I experienced came from.
Sorry forgot to ask about that. I have not seen a "IndexOutOfSync" before, what do you mean exactly? Do you have a stacktrace to post?